Carry across selected updates from development branch

.github/workflows/main.yml

@@ -35,7 +35,7 @@ jobs:
 
       # Check syntax of all CIF files
       - name: Check CIF syntax
-        uses: COMCIFS/cif_syntax_check_action@master
+        uses: COMCIFS/cif_syntax_check_action@main
         id: cif_syntax_check
 
   semantics:

cif_core.dic

@@ -11,7 +11,7 @@ data_CIF_CORE
     _dictionary.title             CIF_CORE
     _dictionary.class             Instance
     _dictionary.version           3.3.0
-    _dictionary.date              2026-07-10
+    _dictionary.date              2026-07-20
     _dictionary.uri
         https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic
     _dictionary.ddl_conformance   4.2.0
@@ -317,25 +317,6 @@ save_diffrn.ambient_temperature_lt
 
 save_
 
-save_diffrn.crystal_id
-
-    _definition.id                '_diffrn.crystal_id'
-    _definition.update            2022-05-09
-    _description.text
-;
-    Identifier for the crystal from which diffraction data were
-    collected. This is a pointer to _exptl_crystal.id.
-;
-    _name.category_id             diffrn
-    _name.object_id               crystal_id
-    _name.linked_item_id          '_exptl_crystal.id'
-    _type.purpose                 Link
-    _type.source                  Assigned
-    _type.container               Single
-    _type.contents                Word
-
-save_
-
 save_diffrn.crystal_support
 
     _definition.id                '_diffrn.crystal_support'
@@ -4914,7 +4895,7 @@ save_diffrn_refln.wavelength_id
     _definition.update            2021-10-27
     _description.text
 ;
-    Code identifying the wavelength in the diffrn_radiation_wavelength list.
+    Code identifying the wavelength in the DIFFRN_RADIATION_WAVELENGTH list.
 ;
     _name.category_id             diffrn_refln
     _name.object_id               wavelength_id
@@ -9967,7 +9948,7 @@ save_CHEMICAL_CONN_ATOM
     the molecular species. They allow a 2D chemical diagram to be
     reconstructed for use in a publication or in a database search
     for structural and substructural relationships. In particular,
-    the chemical_conn_atom data items provide information about the
+    the CHEMICAL_CONN_ATOM data items provide information about the
     chemical properties of the atoms in the structure. In cases
     where crystallographic and molecular symmetry elements coincide
     they must also contain symmetry-generated atoms, so as to describe
@@ -10071,9 +10052,9 @@ save_chemical_conn_atom.nh
 ;
     Total number of hydrogen atoms attached to this atom,
     regardless of whether they are included in the refinement or
-    the atom_site list. This number will be the same as
+    the ATOM_SITE list. This number will be the same as
     _atom_site.attached_hydrogens only if none of the hydrogen
-    atoms appear in the atom_site list.
+    atoms appear in the ATOM_SITE list.
 ;
     _name.category_id             chemical_conn_atom
     _name.object_id               NH
@@ -10134,7 +10115,7 @@ save_CHEMICAL_CONN_BOND
     _description.text
 ;
     The category of data items which specify the connections between
-    the atoms sites in the chemical_conn_atom list and the nature
+    the atoms sites in the CHEMICAL_CONN_ATOM list and the nature
     of the chemical bond between these atoms. These are details about
     the two-dimensional (2D) chemical structure of the molecular species.
     They allow a 2D chemical diagram to be reconstructed for use in a
@@ -10363,10 +10344,10 @@ save_chemical_formula.iupac
 ;
     Formula expressed in conformance with IUPAC rules for inorganic
     and metal-organic compounds where these conflict with the rules
-    for any other chemical_formula entries. Typically used for
+    for any other CHEMICAL_FORMULA entries. Typically used for
     formatting a formula in accordance with journal rules. This
     should appear in the data block in addition to the most
-    appropriate of the other chemical_formula data names.
+    appropriate of the other CHEMICAL_FORMULA data names.
     Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry.
          Oxford: Blackwell Scientific Publications.
 ;
@@ -10788,7 +10769,6 @@ save_EXPTL_CRYSTAL
 ;
     _name.category_id             EXPTL
     _name.object_id               EXPTL_CRYSTAL
-    _category_key.name            '_exptl_crystal.id'
 
 save_
 
@@ -11142,24 +11122,6 @@ save_exptl_crystal.f_000
 
 save_
 
-save_exptl_crystal.id
-
-    _definition.id                '_exptl_crystal.id'
-    _alias.definition_id          '_exptl_crystal_id'
-    _definition.update            2022-05-09
-    _description.text
-;
-    Code identifying a crystal.
-;
-    _name.category_id             exptl_crystal
-    _name.object_id               id
-    _type.purpose                 Key
-    _type.source                  Assigned
-    _type.container               Single
-    _type.contents                Word
-
-save_
-
 save_exptl_crystal.mosaic_block_size
 
     _definition.id                '_exptl_crystal.mosaic_block_size'
@@ -12507,6 +12469,172 @@ save_space_group.point_group_h-m
 
 save_
 
+save_space_group.reference_setting
+
+    _definition.id                '_space_group.reference_setting'
+    _definition.update            2026-07-10
+    _description.text
+;
+    The reference setting of a given space group is the setting
+    chosen by the International Union of Crystallography as a
+    unique setting to which other settings can be referred
+    using the transformation matrix column pair given in
+    _space_group.transform_Pp_abc and _space_group.transform_Qq_xyz.
+
+    The settings are given in the enumeration list in the form
+    '_space_group.IT_number:_space_group.name_Hall'. The
+    space-group number defines the space-group type and the
+    Hall symbol specifies the symmetry generators referred to
+    the reference coordinate system.
+
+    The 230 reference settings chosen are identical to the settings
+    listed in International Tables for Crystallography Volume A
+    (2002). For the space groups where more than one setting is
+    given in International Tables, the following choices have
+    been made.
+
+    For monoclinic space groups: unique axis b and cell choice 1.
+
+    For space groups with two origins: origin choice 2 (origin at
+    inversion centre, indicated by adding :2 to the Hermann-Mauguin
+    symbol in the enumeration list).
+
+    For rhombohedral space groups: hexagonal axes (indicated by
+    adding :h to the Hermann-Mauguin symbol in the enumeration list).
+
+    Based on the symmetry table of R. W. Grosse-Kunstleve, ETH,
+    Zurich.
+
+    In the enumeration list, each reference setting is identified
+    by Schoenflies symbol and by the Hermann-Mauguin symbol,
+    augmented by :2 or :h suffixes as described above.
+
+    Ref: International Tables for Crystallography (2002). Volume A,
+         Space-group symmetry, edited by Th. Hahn, 5th ed.
+         Dordrecht: Kluwer Academic Publishers.
+
+         Grosse-Kunstleve, R. W. (2001). Xtal System of
+         Crystallographic Programs, System Documentation.
+         https://xtal.sourceforge.net/man/symmetry.html
+         (or follow links to Documentation->Xtal Users Manual->Symmetry from
+         https://xtal.sourceforge.net).
+;
+    _name.category_id             space_group
+    _name.object_id               reference_setting
+    _type.purpose                 State
+    _type.source                  Assigned
+    _type.container               Single
+    _type.contents                Text
+
+    _import.get                   [{'file':templ_enum.cif  'save':ref_set}]
+
+save_
+
+save_space_group.transform_pp_abc
+
+    _definition.id                '_space_group.transform_Pp_abc'
+    _definition.update            2026-07-10
+    _description.text
+;
+    This item specifies the transformation (P,p) of the basis
+    vectors from the setting used in the CIF (a,b,c) to the
+    reference setting given in _space_group.reference_setting
+    (a',b',c'). The value is given in Jones faithful notation
+    corresponding to the rotational matrix P combined with the
+    origin shift vector p in the expression:
+
+         (a',b',c') = (a,b,c)P + p.
+
+    P is a post-multiplication matrix of a row (a,b,c) of column
+    vectors. It is related to the inverse transformation (Q,q) by:
+
+         P = Q^-1^
+         p = Pq = -(Q^-1^)q.
+
+    These transformations are applied as follows:
+
+    atomic coordinates  (x',y',z') = Q(x,y,z) + q
+    Miller indices      (h',k',l') = (h,k,l)P
+    symmetry operations         W' = (Q,q)W(P,p)
+    basis vectors       (a',b',c') = (a,b,c)P + p
+
+    This item is given as a character string involving the
+    characters a, b and c with commas separating the expressions
+    for the a', b' and c' vectors. The numeric values may be
+    given as integers, fractions or real numbers. Multiplication
+    is implicit, division must be explicit. White space within
+    the string is optional.
+;
+    _name.category_id             space_group
+    _name.object_id               transform_Pp_abc
+    _type.purpose                 Encode
+    _type.source                  Recorded
+    _type.container               Single
+    _type.contents                Text
+
+    loop_
+      _description_example.case
+      _description_example.detail
+         '-b+c, a+c, -a+b+c'      'R3:r to R3:h'
+         'a-1/4, b-1/4, c-1/4'    'Pnnn:1 to Pnnn:2'
+         'b-1/2, c-1/2, a-1/2'    'Bbab:1 to Ccca:2'
+
+save_
+
+save_space_group.transform_qq_xyz
+
+    _definition.id                '_space_group.transform_Qq_xyz'
+    _definition.update            2026-07-10
+    _description.text
+;
+    This item specifies the transformation (Q,q) of the atomic
+    coordinates from the setting used in the CIF [(x,y,z) referred
+    to the basis vectors (a,b,c)] to the reference setting given in
+    _space_group.reference_setting [(x',y',z') referred to the
+    basis vectors (a',b',c')].
+
+    The value given in Jones faithful notation corresponds to the
+    rotational matrix Q combined with the origin shift vector q in
+    the expression:
+
+        (x',y',z') = Q(x,y,z) + q.
+
+    Q is a pre-multiplication matrix of the column vector (x,y,z).
+    It is related to the inverse transformation (P,p) by:
+
+        P = Q^-1^
+        p = Pq = -(Q^-1^)q,
+
+    where the P and Q transformations are applied as follows:
+
+    atomic coordinates  (x',y',z') = Q(x,y,z) + q
+    Miller indices      (h',k',l') = (h,k,l)P
+    symmetry operations         W' = (Q,q)W(P,p)
+    basis vectors       (a',b',c') = (a,b,c)P + p
+
+    This item is given as a character string involving the
+    characters x, y and z with commas separating the expressions
+    for the x', y' and z' components. The numeric values may be
+    given as integers, fractions or real numbers. Multiplication
+    is implicit, division must be explicit. White space within
+    the string is optional.
+;
+    _name.category_id             space_group
+    _name.object_id               transform_Qq_xyz
+    _type.purpose                 Encode
+    _type.source                  Recorded
+    _type.container               Single
+    _type.contents                Text
+
+    loop_
+      _description_example.case
+      _description_example.detail
+         '-x/3+2y/3-z/3, -2x/3+y/3+z/3, x/3+y/3+z/3'         'R3:r to R3:h'
+         'x+1/4, y+1/4, z+1/4'                               'Pnnn:1 to Pnnn:2'
+         'z+1/2, x+1/2, y+1/2'                               'Bbab:1 to Ccca:2'
+
+save_
+
 save_symmetry.cell_setting
 
     _definition.id                '_symmetry.cell_setting'
@@ -25574,10 +25702,10 @@ save_
 save_atom_type.element_symbol
 
     _definition.id                '_atom_type.element_symbol'
-    _definition.update            2026-04-20
+    _definition.update            2026-07-20
     _description.text
 ;
-    Element symbol for of this atom type. The default value is extracted
+    Element symbol of this atom type. The default value is extracted
     from the ion-to-element enumeration_default list using the index
     value of _atom_type.symbol.
 ;
@@ -25725,14 +25853,16 @@ save_atom_type.symbol
 
     _definition.id                '_atom_type.symbol'
     _alias.definition_id          '_atom_type_symbol'
-    _definition.update            2021-10-27
+    _definition.update            2026-07-19
     _description.text
 ;
     The identity of the atom specie(s) representing this atom type.
     Normally this code is the element symbol followed by the charge
     if there is one. The symbol may be composed of any character except
-    an underline or a blank, with the proviso that digits designate an
-    oxidation state and must be followed by a + or - character.
+    an underline or a blank, with the proviso that digits designate a
+    charge and must be followed by a + or - character.
+
+    Use _atom_type.oxidation_number to indicate the oxidation state.
 ;
     _name.category_id             atom_type
     _name.object_id               symbol
@@ -29384,7 +29514,7 @@ save_
        Changed the purpose of the _diffrn_radiation_wavelength.id data item
        from 'Encode' to 'Key'.
 ;
-         3.3.0                    2026-07-10
+         3.3.0                    2026-07-20
 ;
        Expanded available form factor parameterisations, added support for
        isotopes and symmforms for atom sites. More details can be added
@@ -29459,4 +29589,9 @@ save_
        J. Appl. Cryst. 57, 1733-1746]
 
        Added AUDIT_DATASET for identifying datasets.
+
+       Added _space_group.reference_setting, _space_group.transform_Pp_abc, and
+       _space_group.transform_Qq_xyz from symCIF to SPACE_GROUP.
+
+       Remove _exptl_crystal.id as it is present in multiblock dictionary.
 ;